******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.10.0 (Release date: Wed May 21 10:35:36 2014 +1000) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net. This file may be used as input to the MAST algorithm for searching sequence databases for matches to groups of motifs. MAST is available for interactive use and downloading at http://meme.nbcr.net. ******************************************************************************** ******************************************************************************** REFERENCE ******************************************************************************** If you use this program in your research, please cite: Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. ******************************************************************************** ******************************************************************************** TRAINING SET ******************************************************************************** DATAFILE= motifs/255/255.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 13365 1.0000 500 13662 1.0000 500 2966 1.0000 500 49398 1.0000 500 16018 1.0000 500 49523 1.0000 500 49902 1.0000 500 23623 1.0000 500 54192 1.0000 500 26299 1.0000 500 45268 1.0000 500 11922 1.0000 500 35799 1.0000 500 54511 1.0000 500 42002 1.0000 500 48229 1.0000 500 38809 1.0000 500 36690 1.0000 500 48104 1.0000 500 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme motifs/255/255.seqs.fa -oc motifs/255 -dna -minw 12 -maxw 21 -nmotifs 3 -maxsize 500000 model: mod= zoops nmotifs= 3 evt= inf object function= E-value of product of p-values width: minw= 12 maxw= 21 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 19 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 global: substring= yes branching= no wbranch= no em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 9500 N= 19 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.264 C 0.240 G 0.226 T 0.270 Background letter frequencies (from dataset with add-one prior applied): A 0.264 C 0.240 G 0.226 T 0.270 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 18 sites = 13 llr = 170 E-value = 1.1e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 14a453:8a:42:463:3 pos.-specific C 82:5:25::81:12:::7 probability G 24:245:::228:4271: matrix T ::::1152::4:9:2:9: bits 2.1 1.9 * * 1.7 * * 1.5 * ** ** * Relative 1.3 * *** ** ** Entropy 1.1 * * **** ** *** (18.8 bits) 0.9 * * **** ** *** 0.6 * *** **** ** **** 0.4 ***** **** ******* 0.2 ****************** 0.0 ------------------ Multilevel CAACAGTAACAGTAAGTC consensus G AGAC T GTA A sequence C C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------ 54511 95 1.34e-10 CTGAATACTG CAACAGTAACTGTGAGTC GTTCTCTTGG 54192 266 3.92e-09 TCTACAAACT CCAAGGTAACAGTAAGTC CCGATTCCAA 35799 451 9.43e-09 GCGGGTCATG CGAAACTAACAGTAAGTC ATTTTTCAAT 49902 65 6.88e-08 GCTAGCTAGC GAACAGTAACTGTAAGTA TAGCTAGCTC 36690 35 7.78e-08 CTGGTGTAAC GAAGAGTAACTGTAAGTC ACGTAAGAGA 26299 279 4.43e-07 TGATTATTGG CGACGACAAGAGTGTGTA TGTAGTAGCA 38809 301 6.24e-07 GAAAAGCATT CCAAGCTAACTGTCTGTA CTCCTTTCCG 45268 341 1.00e-06 TATCCCGCGC CGACAACAACGATGAATA CACAGAGAAT 23623 63 1.54e-06 CGCAGCCGCC AAAGGGCAACAATGAGTC GCGCTAGTCC 11922 344 1.65e-06 AGACGACCAG CGACAACAAGAGCAAATC TAACACCACA 42002 145 3.27e-06 CTCAAGAGTA CGAAATCTACCGTGGGTC AACCACACTC 48104 125 3.66e-06 AGTCCTGTTG CCAAGACTACGGTCGATC TTCTCGCGGG 2966 44 3.66e-06 TCCAATTTGC CAACTGTAACTGTCTAGC TCGCGTTTTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 54511 1.3e-10 94_[+1]_388 54192 3.9e-09 265_[+1]_217 35799 9.4e-09 450_[+1]_32 49902 6.9e-08 64_[+1]_418 36690 7.8e-08 34_[+1]_448 26299 4.4e-07 278_[+1]_204 38809 6.2e-07 300_[+1]_182 45268 1e-06 340_[+1]_142 23623 1.5e-06 62_[+1]_420 11922 1.7e-06 343_[+1]_139 42002 3.3e-06 144_[+1]_338 48104 3.7e-06 124_[+1]_358 2966 3.7e-06 43_[+1]_439 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=18 seqs=13 54511 ( 95) CAACAGTAACTGTGAGTC 1 54192 ( 266) CCAAGGTAACAGTAAGTC 1 35799 ( 451) CGAAACTAACAGTAAGTC 1 49902 ( 65) GAACAGTAACTGTAAGTA 1 36690 ( 35) GAAGAGTAACTGTAAGTC 1 26299 ( 279) CGACGACAAGAGTGTGTA 1 38809 ( 301) CCAAGCTAACTGTCTGTA 1 45268 ( 341) CGACAACAACGATGAATA 1 23623 ( 63) AAAGGGCAACAATGAGTC 1 11922 ( 344) CGACAACAAGAGCAAATC 1 42002 ( 145) CGAAATCTACCGTGGGTC 1 48104 ( 125) CCAAGACTACGGTCGATC 1 2966 ( 44) CAACTGTAACTGTCTAGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 18 n= 9177 bayes= 9.21653 E= 1.1e-003 -177 168 -56 -1035 54 -6 77 -1035 192 -1035 -1035 -1035 54 94 -56 -1035 103 -1035 77 -181 22 -64 103 -181 -1035 94 -1035 100 168 -1035 -1035 -81 192 -1035 -1035 -1035 -1035 181 -56 -1035 54 -164 -56 51 -78 -1035 190 -1035 -1035 -164 -1035 177 54 -6 77 -1035 122 -1035 -56 -22 22 -1035 161 -1035 -1035 -1035 -155 177 22 153 -1035 -1035 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 18 nsites= 13 E= 1.1e-003 0.076923 0.769231 0.153846 0.000000 0.384615 0.230769 0.384615 0.000000 1.000000 0.000000 0.000000 0.000000 0.384615 0.461538 0.153846 0.000000 0.538462 0.000000 0.384615 0.076923 0.307692 0.153846 0.461538 0.076923 0.000000 0.461538 0.000000 0.538462 0.846154 0.000000 0.000000 0.153846 1.000000 0.000000 0.000000 0.000000 0.000000 0.846154 0.153846 0.000000 0.384615 0.076923 0.153846 0.384615 0.153846 0.000000 0.846154 0.000000 0.000000 0.076923 0.000000 0.923077 0.384615 0.230769 0.384615 0.000000 0.615385 0.000000 0.153846 0.230769 0.307692 0.000000 0.692308 0.000000 0.000000 0.000000 0.076923 0.923077 0.307692 0.692308 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[AGC]A[CA][AG][GA][TC]AAC[AT]GT[AGC][AT][GA]T[CA] -------------------------------------------------------------------------------- Time 3.34 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 10 llr = 143 E-value = 7.8e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 21::6:7:11:454::::1:: pos.-specific C :44::91:59:12:::142:2 probability G 113a111a::8511183:296 matrix T 743:3:1:4:2:259266512 bits 2.1 * * 1.9 * * 1.7 * * * 1.5 * * * * * * Relative 1.3 * * * ** ** * Entropy 1.1 * * * ** ** * * (20.7 bits) 0.9 * * * * ** ** * * 0.6 * ********* ***** ** 0.4 * ********** ***** ** 0.2 ********************* 0.0 --------------------- Multilevel TCCGACAGCCGGATTGTTTGG consensus ATG T T TACA TGCC C sequence T T G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 26299 63 5.65e-09 CACGCGCCTC TCCGGCAGCCGGCGTGTTTGG ATAGCTTCAT 49902 117 3.41e-08 AGAGAAATCG TCCGACAGCCGAATGTGTGGG ATTTACCTTG 16018 397 3.41e-08 ATACCCAACA ATCGACAGCCGATTTGGTCGC AAAAATTGTT 49523 329 4.60e-08 TGGATCGACC TATGACAGACGACATGGTTGG ACCAATCCCA 54192 45 5.07e-08 CATTGCGACG TGGGTCAGTCGGGTTGCTTGG CTGCAAAGGC 36690 232 8.85e-08 GGACTGTCTG TCTGTCTGTCTGTTTGTCTGG TGTGTTGGAC 13365 27 1.26e-07 CGTTTCGACT TTGGAGCGTCGGAATGTCTGT CGCGCAAGGT 35799 351 1.37e-07 TAAATGACTA GCGGACAGTCGGAATGTTATG TACCATCGTT 13662 27 4.71e-07 GAGATCCCTT ATTGTCAGCCTCATTGTCGGC AACACGGAGA 48229 400 9.72e-07 GAAGGTCATT TTCGACGGCAGAAATTTCCGT TTTTCACTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 26299 5.7e-09 62_[+2]_417 49902 3.4e-08 116_[+2]_363 16018 3.4e-08 396_[+2]_83 49523 4.6e-08 328_[+2]_151 54192 5.1e-08 44_[+2]_435 36690 8.9e-08 231_[+2]_248 13365 1.3e-07 26_[+2]_453 35799 1.4e-07 350_[+2]_129 13662 4.7e-07 26_[+2]_453 48229 9.7e-07 399_[+2]_80 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=10 26299 ( 63) TCCGGCAGCCGGCGTGTTTGG 1 49902 ( 117) TCCGACAGCCGAATGTGTGGG 1 16018 ( 397) ATCGACAGCCGATTTGGTCGC 1 49523 ( 329) TATGACAGACGACATGGTTGG 1 54192 ( 45) TGGGTCAGTCGGGTTGCTTGG 1 36690 ( 232) TCTGTCTGTCTGTTTGTCTGG 1 13365 ( 27) TTGGAGCGTCGGAATGTCTGT 1 35799 ( 351) GCGGACAGTCGGAATGTTATG 1 13662 ( 27) ATTGTCAGCCTCATTGTCGGC 1 48229 ( 400) TTCGACGGCAGAAATTTCCGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 9120 bayes= 10.0831 E= 7.8e+001 -40 -997 -118 138 -140 73 -118 57 -997 73 41 15 -997 -997 214 -997 119 -997 -118 15 -997 190 -118 -997 141 -126 -118 -143 -997 -997 214 -997 -140 106 -997 57 -140 190 -997 -997 -997 -997 182 -43 60 -126 114 -997 92 -27 -118 -43 60 -997 -118 89 -997 -997 -118 174 -997 -997 182 -43 -997 -126 41 115 -997 73 -997 115 -140 -27 -18 89 -997 -997 199 -143 -997 -27 141 -43 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 10 E= 7.8e+001 0.200000 0.000000 0.100000 0.700000 0.100000 0.400000 0.100000 0.400000 0.000000 0.400000 0.300000 0.300000 0.000000 0.000000 1.000000 0.000000 0.600000 0.000000 0.100000 0.300000 0.000000 0.900000 0.100000 0.000000 0.700000 0.100000 0.100000 0.100000 0.000000 0.000000 1.000000 0.000000 0.100000 0.500000 0.000000 0.400000 0.100000 0.900000 0.000000 0.000000 0.000000 0.000000 0.800000 0.200000 0.400000 0.100000 0.500000 0.000000 0.500000 0.200000 0.100000 0.200000 0.400000 0.000000 0.100000 0.500000 0.000000 0.000000 0.100000 0.900000 0.000000 0.000000 0.800000 0.200000 0.000000 0.100000 0.300000 0.600000 0.000000 0.400000 0.000000 0.600000 0.100000 0.200000 0.200000 0.500000 0.000000 0.000000 0.900000 0.100000 0.000000 0.200000 0.600000 0.200000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TA][CT][CGT]G[AT]CAG[CT]C[GT][GA][ACT][TA]T[GT][TG][TC][TCG]G[GCT] -------------------------------------------------------------------------------- Time 6.40 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 7 llr = 116 E-value = 1.4e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::41:::116334:1::1:: pos.-specific C ::::1:17:31:3::169::1 probability G 1aa6:::39337141611:9: matrix T 9:::7a9::3::31913:919 bits 2.1 ** 1.9 ** * 1.7 ** * 1.5 ** * * * * Relative 1.3 *** **** * * **** Entropy 1.1 **** **** * * **** (23.9 bits) 0.9 ********* * * **** 0.6 ********* ** ** ***** 0.4 ********* ** ******** 0.2 ********* ** ******** 0.0 --------------------- Multilevel TGGGTTTCGCAGAATGCCTGT consensus A G GGACG T sequence T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 13662 168 8.85e-12 TCAGTTTCCG TGGATTTCGTAGTGTGCCTGT TCCCCAAAGT 26299 340 8.71e-10 AGCAGAGCAA TGGGATTCGAGGAATGCCTGT GTCCCTCTAG 48104 32 1.43e-08 TTGATGTTAA GGGGTTTGGGGGGAGGCCTGT TCCAATTGCA 54511 125 1.96e-08 TCTCTTGGTA TGGATTCGGGAATGTACCTGT TTTTCCAGAG 13365 234 3.09e-08 ACGGACTGTT TGGGTTTCGCAGCGTGTCATC CCGGACGCAA 45268 465 4.70e-08 AAAGGAGCGT TGGATTTCGCAACTTTTGTGT GCAGTCTTAA 2966 276 1.11e-07 ATCCCAGTAG TGGGCTTCATCGAATCGCTGT CCTTTTTTCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 13662 8.8e-12 167_[+3]_312 26299 8.7e-10 339_[+3]_140 48104 1.4e-08 31_[+3]_448 54511 2e-08 124_[+3]_355 13365 3.1e-08 233_[+3]_246 45268 4.7e-08 464_[+3]_15 2966 1.1e-07 275_[+3]_204 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=7 13662 ( 168) TGGATTTCGTAGTGTGCCTGT 1 26299 ( 340) TGGGATTCGAGGAATGCCTGT 1 48104 ( 32) GGGGTTTGGGGGGAGGCCTGT 1 54511 ( 125) TGGATTCGGGAATGTACCTGT 1 13365 ( 234) TGGGTTTCGCAGCGTGTCATC 1 45268 ( 465) TGGATTTCGCAACTTTTGTGT 1 2966 ( 276) TGGGCTTCATCGAATCGCTGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 9120 bayes= 10.1901 E= 1.4e+002 -945 -945 -66 167 -945 -945 214 -945 -945 -945 214 -945 70 -945 134 -945 -88 -75 -945 140 -945 -945 -945 189 -945 -75 -945 167 -945 157 34 -945 -88 -945 192 -945 -88 25 34 8 111 -75 34 -945 12 -945 166 -945 12 25 -66 8 70 -945 92 -91 -945 -945 -66 167 -88 -75 134 -91 -945 125 -66 8 -945 183 -66 -945 -88 -945 -945 167 -945 -945 192 -91 -945 -75 -945 167 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 7 E= 1.4e+002 0.000000 0.000000 0.142857 0.857143 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.428571 0.000000 0.571429 0.000000 0.142857 0.142857 0.000000 0.714286 0.000000 0.000000 0.000000 1.000000 0.000000 0.142857 0.000000 0.857143 0.000000 0.714286 0.285714 0.000000 0.142857 0.000000 0.857143 0.000000 0.142857 0.285714 0.285714 0.285714 0.571429 0.142857 0.285714 0.000000 0.285714 0.000000 0.714286 0.000000 0.285714 0.285714 0.142857 0.285714 0.428571 0.000000 0.428571 0.142857 0.000000 0.000000 0.142857 0.857143 0.142857 0.142857 0.571429 0.142857 0.000000 0.571429 0.142857 0.285714 0.000000 0.857143 0.142857 0.000000 0.142857 0.000000 0.000000 0.857143 0.000000 0.000000 0.857143 0.142857 0.000000 0.142857 0.000000 0.857143 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- TGG[GA]TTT[CG]G[CGT][AG][GA][ACT][AG]TG[CT]CTGT -------------------------------------------------------------------------------- Time 9.59 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 13365 1.06e-07 26_[+2(1.26e-07)]_186_\ [+3(3.09e-08)]_246 13662 3.01e-10 26_[+2(4.71e-07)]_120_\ [+3(8.85e-12)]_312 2966 3.58e-07 43_[+1(3.66e-06)]_214_\ [+3(1.11e-07)]_56_[+2(3.52e-05)]_127 49398 2.45e-01 500 16018 6.13e-04 396_[+2(3.41e-08)]_83 49523 3.34e-04 328_[+2(4.60e-08)]_151 49902 3.69e-08 64_[+1(6.88e-08)]_34_[+2(3.41e-08)]_\ 363 23623 1.38e-02 62_[+1(1.54e-06)]_420 54192 3.09e-09 44_[+2(5.07e-08)]_200_\ [+1(3.92e-09)]_217 26299 1.66e-13 29_[+3(9.27e-05)]_12_[+2(5.65e-09)]_\ 195_[+1(4.43e-07)]_43_[+3(8.71e-10)]_140 45268 1.70e-06 340_[+1(1.00e-06)]_106_\ [+3(4.70e-08)]_15 11922 1.29e-03 343_[+1(1.65e-06)]_139 35799 4.45e-08 350_[+2(1.37e-07)]_79_\ [+1(9.43e-09)]_32 54511 2.16e-10 94_[+1(1.34e-10)]_12_[+3(1.96e-08)]_\ 355 42002 2.22e-02 144_[+1(3.27e-06)]_338 48229 3.23e-03 399_[+2(9.72e-07)]_80 38809 3.93e-03 300_[+1(6.24e-07)]_182 36690 2.37e-07 34_[+1(7.78e-08)]_179_\ [+2(8.85e-08)]_248 48104 8.73e-07 31_[+3(1.43e-08)]_72_[+1(3.66e-06)]_\ 358 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************